Remove UI elements deprecated since 3.9 (#3256)

* Remove UI elements deprecated since 3.9

* Add change log

* Remove deprecated save as fits in spectral extraction plugin

* Remove unused tooltips

* Remove unused vue write methods

* Update tests after removing the deprecated methods

* Update change log

* Update tests and fix code style

* Update changelog

* Update the changelog

CHANGES.rst

@@ -44,6 +44,7 @@ Bug Fixes
 
 Cubeviz
 ^^^^^^^
+- Removed the deprecated ``save as fits`` option from the Collapse, Moment Maps, and Spectral Extraction plugins; use the Export plugin instead. [#3256]
 
 Imviz
 ^^^^^

jdaviz/app.vue

@@ -114,7 +114,7 @@
                   <div v-if="trayItem.is_relevant && trayItemVisible(trayItem, state.tray_items_filter)">
                     <v-expansion-panel-header >
                       <j-tooltip :tipid="trayItem.name">
-                        {{ trayItem.label == 'Orientation' ? 'Orientation (prev. Links Control)' : trayItem.label }}
+                        {{ trayItem.label }}
                       </j-tooltip>
                     </v-expansion-panel-header>
                     <v-expansion-panel-content style="margin-left: -12px; margin-right: -12px;">

jdaviz/components/tooltip.vue

@@ -101,9 +101,7 @@ const tooltips = {
   'plugin-line-lists-spectral-range': 'Toggle filter to only lines observable within the range of the Spectrum Viewer',
   'plugin-line-analysis-sync-identify': 'Lock/unlock selection with identified line',
   'plugin-line-analysis-assign': 'Assign the centroid wavelength and update the redshift',
-  'plugin-moment-save-fits': 'Save moment map as FITS file',
   'plugin-extract-save-fits': 'Save spectral extraction as FITS file',
-  'plugin-collapse-save-fits': 'Save collapsed cube as FITS file',
   'plugin-link-apply': 'Apply linking to data',
   'plugin-footprints-color-picker': 'Change the color of the footprint overlay',
   'plugin-dq-show-all': 'Show all quality flags',

jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.py

@@ -1,6 +1,3 @@
-import os
-from pathlib import Path
-
 import numpy as np
 import specutils
 from astropy import units as u
@@ -80,7 +77,6 @@ class MomentMap(PluginTemplateMixin, DatasetSelectMixin, SpectralSubsetSelectMix
     n_moment = IntHandleEmpty(0).tag(sync=True)
     filename = Unicode().tag(sync=True)
     moment_available = Bool(False).tag(sync=True)
-    overwrite_warn = Bool(False).tag(sync=True)
     output_unit_items = List().tag(sync=True)
     output_radio_items = List().tag(sync=True)
     output_unit_selected = Unicode().tag(sync=True)
@@ -360,45 +356,6 @@ def spectral_unit_selected(self):
     def vue_calculate_moment(self, *args):
         self.calculate_moment(add_data=True)
 
-    def vue_save_as_fits(self, *args):
-        self._write_moment_to_fits()
-
     def vue_overwrite_fits(self, *args):
         """Attempt to force writing the moment map if the user confirms the desire to overwrite."""
         self.overwrite_warn = False
-        self._write_moment_to_fits(overwrite=True)
-
-    def _write_moment_to_fits(self, overwrite=False, *args):
-        if self.moment is None or not self.filename:  # pragma: no cover
-            return
-        if not self.export_enabled:
-            # this should never be triggered since this is intended for UI-disabling and the
-            # UI section is hidden, but would prevent any JS-hacking
-            raise ValueError("Writing out moment map to file is currently disabled")
-
-        # Make sure file does not end up in weird places in standalone mode.
-        path = os.path.dirname(self.filename)
-        if path and not os.path.exists(path):
-            raise ValueError(f"Invalid path={path}")
-        elif (not path or path.startswith("..")) and os.environ.get("JDAVIZ_START_DIR", ""):  # noqa: E501 # pragma: no cover
-            filename = Path(os.environ["JDAVIZ_START_DIR"]) / self.filename
-        else:
-            filename = Path(self.filename).resolve()
-
-        if filename.exists():
-            if overwrite:
-                # Try to delete the file
-                filename.unlink()
-                if filename.exists():
-                    # Warn the user if the file still exists
-                    raise FileExistsError(f"Unable to delete {filename}. Check user permissions.")
-            else:
-                self.overwrite_warn = True
-                return
-
-        filename = str(filename)
-        self.moment.write(filename)
-
-        # Let the user know where we saved the file.
-        self.hub.broadcast(SnackbarMessage(
-            f"Moment map saved to {os.path.abspath(filename)}", sender=self, color="success"))

jdaviz/configs/cubeviz/plugins/moment_maps/moment_maps.vue

@@ -173,65 +173,5 @@
           Cannot calculate moment: Must set reference wavelength for output in velocity units.
       </span>
     </v-row>
-
-    <j-plugin-section-header v-if="moment_available && export_enabled">Results</j-plugin-section-header>
-
-    <div style="display: grid; position: relative"> <!-- overlay container -->
-      <div style="grid-area: 1/1">
-        <div v-if="moment_available && export_enabled">
-          <v-row>
-              <v-text-field
-              v-model="filename"
-              label="Filename"
-              hint="Export the latest calculated moment map"
-              :rules="[() => !!filename || 'This field is required']"
-              persistent-hint>
-              </v-text-field>
-          </v-row>
-
-          <v-row>
-            <span class="v-messages v-messages__message text--secondary" style="color: red !important">
-                DeprecationWarning: Save as FITS functionality has moved to the Export plugin as of v3.9 and will be removed from Moment Maps plugin in a future release.
-            </span>
-          </v-row>
-
-          <v-row justify="end">
-            <j-tooltip tipid='plugin-moment-save-fits'>
-              <v-btn color="primary" text @click="save_as_fits">Save as FITS</v-btn>
-
-            </j-tooltip>
-          </v-row>
-
-        </div>
-      </div>
-
-      <v-overlay
-        absolute
-        opacity=1.0
-        :value="overwrite_warn && export_enabled"
-        :zIndex=3
-        style="grid-area: 1/1;
-               margin-left: -24px;
-               margin-right: -24px">
-
-      <v-card color="transparent" elevation=0 >
-        <v-card-text width="100%">
-          <div class="white--text">
-            A file with this name is already on disk. Overwrite?
-          </div>
-        </v-card-text>
-
-        <v-card-actions>
-          <v-row justify="end">
-            <v-btn tile small color="primary" class="mr-2" @click="overwrite_warn=false">Cancel</v-btn>
-            <v-btn tile small color="accent" class="mr-4" @click="overwrite_fits" >Overwrite</v-btn>
-          </v-row>
-        </v-card-actions>
-      </v-card>
-
-      </v-overlay>
-
-
-    </div>
   </j-tray-plugin>
 </template>

jdaviz/configs/cubeviz/plugins/moment_maps/tests/test_moment_maps.py

@@ -1,11 +1,9 @@
-import os
 import warnings
 from pathlib import Path
 
 import numpy as np
 import pytest
 from astropy import units as u
-from astropy.io import fits
 from astropy.nddata import CCDData
 from astropy.tests.helper import assert_quantity_allclose
 from astropy.wcs import WCS
@@ -144,11 +142,6 @@ def test_moment_calculation(cubeviz_helper, spectrum1d_cube,
         "World 13h39m59.9731s +27d00m00.3600s (ICRS)",
         "204.9998877673 27.0001000000 (deg)")
 
-    assert mm._obj.filename == 'moment0_test_FLUX.fits'  # Auto-populated on calculate.
-    mm._obj.filename = str(tmp_path / mm._obj.filename)  # But we want it in tmp_path for testing.
-    mm._obj.vue_save_as_fits()
-    assert os.path.isfile(mm._obj.filename)
-
     mm._obj.n_moment = 1
     mm._obj.output_unit_selected = "Spectral Unit"
     assert mm._obj.results_label == 'moment 1'
@@ -258,42 +251,22 @@ def test_write_momentmap(cubeviz_helper, spectrum1d_cube, tmp_path):
 
     # Simulate an existing file on disk to check for overwrite warning
     test_file = tmp_path / "test_file.fits"
-    test_file_str = str(test_file)
     existing_sentinel_text = "This is a simulated, existing file on disk"
     test_file.write_text(existing_sentinel_text)
 
     with warnings.catch_warnings():
         warnings.filterwarnings("ignore", message="No observer defined on WCS.*")
         cubeviz_helper.load_data(spectrum1d_cube, data_label='test')
     plugin = cubeviz_helper.plugins['Moment Maps']
-    moment = plugin.calculate_moment()
-
-    # By default, we shouldn't be warning the user of anything
-    assert plugin._obj.overwrite_warn is False
+    plugin.calculate_moment()
 
-    # Attempt to write the moment map to the same file we created earlier.
-    plugin._obj.filename = test_file_str
-    plugin._obj.vue_save_as_fits()
-
-    # We should get an overwrite warning
-    assert plugin._obj.overwrite_warn is True
     # and shouldn't have written anything (the file should be intact)
     assert test_file.read_text() == existing_sentinel_text
 
-    # Force overwrite the existing file
-    plugin._obj.vue_overwrite_fits()
-
-    # Read back in the file and check that it is equal to the one we calculated
-    with fits.open(test_file_str) as pf:
-        assert_allclose(pf[0].data, moment.data)
-        w = WCS(pf[0].header)
-        sky = w.pixel_to_world(0, 0)
-        assert_allclose(sky.ra.deg, 204.9998877673)
-        assert_allclose(sky.dec.deg, 27.0001)
+    label = plugin._obj.add_results.label
+    export_plugin = cubeviz_helper.plugins['Export']._obj
 
-    plugin._obj.filename = "fake_path/test_file.fits"
-    with pytest.raises(ValueError, match="Invalid path"):
-        plugin._obj.vue_save_as_fits()
+    assert label in export_plugin.data_collection.labels
 
 
 @pytest.mark.remote_data

jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.py

@@ -1,6 +1,4 @@
-import os
 from functools import cached_property
-from pathlib import Path
 
 import numpy as np
 import astropy
@@ -105,7 +103,6 @@ class SpectralExtraction(PluginTemplateMixin, ApertureSubsetSelectMixin,
     function_selected = Unicode('Sum').tag(sync=True)
     filename = Unicode().tag(sync=True)
     extraction_available = Bool(False).tag(sync=True)
-    overwrite_warn = Bool(False).tag(sync=True)
 
     results_units = Unicode().tag(sync=True)
     spectrum_y_units = Unicode().tag(sync=True)
@@ -672,50 +669,6 @@ def vue_spectral_extraction(self, *args, **kwargs):
     def vue_create_bg_spec(self, *args, **kwargs):
         self.extract_bg_spectrum(add_data=True)
 
-    def vue_save_as_fits(self, *args):
-        self._save_extracted_spec_to_fits()
-
-    def vue_overwrite_fits(self, *args):
-        """Attempt to force writing the spectral extraction if the user
-        confirms the desire to overwrite."""
-        self.overwrite_warn = False
-        self._save_extracted_spec_to_fits(overwrite=True)
-
-    def _save_extracted_spec_to_fits(self, overwrite=False, *args):
-
-        if not self.export_enabled:
-            # this should never be triggered since this is intended for UI-disabling and the
-            # UI section is hidden, but would prevent any JS-hacking
-            raise ValueError(f"Writing out extracted {self.resulting_product_name} to file is currently disabled")  # noqa
-
-        # Make sure file does not end up in weird places in standalone mode.
-        path = os.path.dirname(self.filename)
-        if path and not os.path.exists(path):
-            raise ValueError(f"Invalid path={path}")
-        elif (not path or path.startswith("..")) and os.environ.get("JDAVIZ_START_DIR", ""):  # noqa: E501 # pragma: no cover
-            filename = Path(os.environ["JDAVIZ_START_DIR"]) / self.filename
-        else:
-            filename = Path(self.filename).resolve()
-
-        if filename.exists():
-            if overwrite:
-                # Try to delete the file
-                filename.unlink()
-                if filename.exists():
-                    # Warn the user if the file still exists
-                    raise FileExistsError(f"Unable to delete {filename}. Check user permissions.")
-            else:
-                self.overwrite_warn = True
-                return
-
-        filename = str(filename)
-        self.extracted_spec.write(filename)
-
-        # Let the user know where we saved the file.
-        self.hub.broadcast(SnackbarMessage(
-            f"Extracted {self.resulting_product_name} saved to {os.path.abspath(filename)}",
-            sender=self, color="success"))
-
     @observe('aperture_selected', 'function_selected')
     def _set_default_results_label(self, event={}):
         if not hasattr(self, 'aperture'):

jdaviz/configs/cubeviz/plugins/spectral_extraction/spectral_extraction.vue

@@ -271,65 +271,5 @@
         </v-alert>
       </plugin-add-results>
 
-      <j-plugin-section-header v-if="extraction_available && export_enabled">Results</j-plugin-section-header>
-
-      <div style="display: grid; position: relative"> <!-- overlay container -->
-        <div style="grid-area: 1/1">
-          <div v-if="extraction_available && export_enabled">
-
-            <v-row>
-              <v-text-field
-              v-model="filename"
-              label="Filename"
-              hint="Export the latest extracted spectrum."
-              :rules="[() => !!filename || 'This field is required']"
-              persistent-hint>
-              </v-text-field>
-            </v-row>
-
-            <v-row>
-              <span class="v-messages v-messages__message text--secondary" style="color: red !important">
-                DeprecationWarning: Save as FITS functionality has moved to the Export plugin as of v3.9 and will be removed from here in a future release.
-              </span>
-            </v-row>
-
-            <v-row justify="end">
-              <j-tooltip tipid='plugin-extract-save-fits'>
-                <v-btn color="primary" text @click="save_as_fits">Save as FITS</v-btn>
-
-              </j-tooltip>
-            </v-row>
-
-          </div>
-        </div>
-
-        <v-overlay
-          absolute
-          opacity=1.0
-          :value="overwrite_warn && export_enabled"
-          :zIndex=3
-          style="grid-area: 1/1;
-                 margin-left: -24px;
-                 margin-right: -24px">
-
-        <v-card color="transparent" elevation=0 >
-          <v-card-text width="100%">
-            <div class="white--text">
-              A file with this name is already on disk. Overwrite?
-            </div>
-          </v-card-text>
-
-          <v-card-actions>
-            <v-row justify="end">
-              <v-btn tile small color="primary" class="mr-2" @click="overwrite_warn=false">Cancel</v-btn>
-              <v-btn tile small color="accent" class="mr-4" @click="overwrite_fits" >Overwrite</v-btn>
-            </v-row>
-          </v-card-actions>
-        </v-card>
-
-        </v-overlay>
-      </div>
-    </div>
-
   </j-tray-plugin>
 </template>